forked from lijiext/lammps
234 lines
5.5 KiB
Fortran
234 lines
5.5 KiB
Fortran
c Create LAMMPS 2003 input file for 2d LJ simulation of micelles
|
|
c
|
|
c Syntax: micelle2d < def.micelle2d > data.file
|
|
c
|
|
c def file contains size of system and number to turn into surfactants
|
|
c attaches a random surfactant tail(s) to random head
|
|
c if nonflag is set, will attach 2nd-neighbor bonds in surfactant
|
|
c solvent atoms = type 1
|
|
c micelle heads = type 2
|
|
c micelle tails = type 3,4,5,etc.
|
|
|
|
program micelle2d
|
|
parameter (maxatom=100000,maxbond=10000)
|
|
real*4 x(2,maxatom)
|
|
integer type(maxatom),molecule(maxatom)
|
|
integer bondatom(2,maxbond),bondtype(maxbond)
|
|
common xprd,yprd,zprd,xboundlo,xboundhi,yboundlo,yboundhi,
|
|
$ zboundlo,zboundhi
|
|
999 format (3i7,3f8.3)
|
|
998 format (4i7)
|
|
|
|
read (5,*)
|
|
read (5,*)
|
|
read (5,*) rhostar
|
|
read (5,*) iseed
|
|
read (5,*) nx,ny
|
|
read (5,*) nsurf
|
|
read (5,*) r0
|
|
read (5,*) ntails
|
|
read (5,*) nonflag
|
|
|
|
natoms = nx*ny
|
|
if (natoms+nsurf*ntails.gt.maxatom) then
|
|
write (6,*) 'Too many atoms - boost maxatom'
|
|
call exit(0)
|
|
endif
|
|
|
|
nbonds = nsurf*ntails
|
|
if (nonflag.eq.1) nbonds = nbonds + nsurf*(ntails-1)
|
|
if (nbonds.gt.maxbond) then
|
|
write (6,*) 'Too many surfactants - boost maxbond'
|
|
call exit(0)
|
|
endif
|
|
|
|
c box size
|
|
|
|
rlattice = (1.0/rhostar) ** 0.5
|
|
|
|
xboundlo = 0.0
|
|
xboundhi = nx*rlattice
|
|
yboundlo = 0.0
|
|
yboundhi = ny*rlattice
|
|
zboundlo = -0.1
|
|
zboundhi = 0.1
|
|
|
|
sigma = 1.0
|
|
|
|
xprd = xboundhi - xboundlo
|
|
yprd = yboundhi - yboundlo
|
|
zprd = zboundhi - zboundlo
|
|
|
|
c initial square lattice of solvents
|
|
|
|
m = 0
|
|
do j = 1,ny
|
|
do i = 1,nx
|
|
m = m + 1
|
|
x(1,m) = xboundlo + (i-1)*rlattice
|
|
x(2,m) = yboundlo + (j-1)*rlattice
|
|
molecule(m) = 0
|
|
type(m) = 1
|
|
enddo
|
|
enddo
|
|
|
|
c turn some into surfactants with molecule ID
|
|
c head changes to type 2
|
|
c create ntails for each head of types 3,4,...
|
|
c each tail is at distance r0 away in straight line with random orientation
|
|
|
|
do i = 1,nsurf
|
|
|
|
10 m = random(iseed)*natoms + 1
|
|
if (m.gt.natoms) m = natoms
|
|
if (molecule(m) .ne. 0) goto 10
|
|
|
|
molecule(m) = i
|
|
type(m) = 2
|
|
|
|
angle = random(iseed)*2.0*3.1415926
|
|
do j = 1,ntails
|
|
k = (i-1)*ntails + j
|
|
x(1,natoms+k) = x(1,m) + cos(angle)*j*r0*sigma
|
|
x(2,natoms+k) = x(2,m) + sin(angle)*j*r0*sigma
|
|
molecule(natoms+k) = i
|
|
type(natoms+k) = 2+j
|
|
call pbc(x(1,natoms+k),x(2,natoms+k))
|
|
if (j.eq.1) bondatom(1,k) = m
|
|
if (j.ne.1) bondatom(1,k) = natoms+k-1
|
|
bondatom(2,k) = natoms+k
|
|
bondtype(k) = 1
|
|
enddo
|
|
|
|
enddo
|
|
|
|
c if nonflag is set, add (ntails-1) 2nd nearest neighbor bonds to end
|
|
c of bond list
|
|
c k = location in bondatom list where nearest neighbor bonds for
|
|
c this surfactant are stored
|
|
|
|
if (nonflag.eq.1) then
|
|
|
|
nbonds = nsurf*ntails
|
|
do i = 1,nsurf
|
|
do j = 1,ntails-1
|
|
k = (i-1)*ntails + j
|
|
nbonds = nbonds + 1
|
|
bondatom(1,nbonds) = bondatom(1,k)
|
|
bondatom(2,nbonds) = bondatom(2,k+1)
|
|
bondtype(nbonds) = 2
|
|
enddo
|
|
enddo
|
|
|
|
endif
|
|
|
|
c write LAMMPS data file
|
|
|
|
natoms = natoms + nsurf*ntails
|
|
nbonds = nsurf*ntails
|
|
if (nonflag.eq.1) nbonds = nbonds + nsurf*(ntails-1)
|
|
ntypes = 2 + ntails
|
|
nbondtypes = 1
|
|
if (nonflag.eq.1) nbondtypes = 2
|
|
|
|
if (nsurf.eq.0) then
|
|
ntypes = 1
|
|
nbondtypes = 0
|
|
endif
|
|
|
|
write (6,*) 'LAMMPS 2d micelle data file'
|
|
write (6,*)
|
|
|
|
write (6,*) natoms,' atoms'
|
|
write (6,*) nbonds,' bonds'
|
|
write (6,*) 0,' angles'
|
|
write (6,*) 0,' dihedrals'
|
|
write (6,*) 0,' impropers'
|
|
write (6,*)
|
|
|
|
write (6,*) ntypes,' atom types'
|
|
write (6,*) nbondtypes,' bond types'
|
|
write (6,*) 0,' angle types'
|
|
write (6,*) 0,' dihedral types'
|
|
write (6,*) 0,' improper types'
|
|
write (6,*)
|
|
|
|
write (6,*) xboundlo,xboundhi,' xlo xhi'
|
|
write (6,*) yboundlo,yboundhi,' ylo yhi'
|
|
write (6,*) zboundlo,zboundhi,' zlo zhi'
|
|
|
|
write (6,*)
|
|
write (6,*) 'Masses'
|
|
write (6,*)
|
|
|
|
do i = 1,ntypes
|
|
write (6,*) i,1.0
|
|
enddo
|
|
|
|
write (6,*)
|
|
write (6,*) 'Atoms'
|
|
write (6,*)
|
|
|
|
do i = 1,natoms
|
|
write (6,999) i,molecule(i),type(i),x(1,i),x(2,i),0.0
|
|
enddo
|
|
|
|
if (nsurf.gt.0) then
|
|
|
|
write (6,*)
|
|
write (6,*) 'Bonds'
|
|
write (6,*)
|
|
|
|
do i = 1,nbonds
|
|
write (6,998) i,bondtype(i),bondatom(1,i),bondatom(2,i)
|
|
enddo
|
|
|
|
endif
|
|
|
|
c write Xmovie bond geometry file
|
|
|
|
open(1,file='bond.micelle')
|
|
|
|
write (1,*) 'ITEM: BONDS'
|
|
do i = 1,nbonds
|
|
write (1,*) bondtype(i),bondatom(1,i),bondatom(2,i)
|
|
enddo
|
|
|
|
close(1)
|
|
|
|
end
|
|
|
|
|
|
c ************
|
|
c Subroutines
|
|
c ************
|
|
|
|
c periodic boundary conditions - map atom back into periodic box
|
|
|
|
subroutine pbc(x,y)
|
|
common xprd,yprd,zprd,xboundlo,xboundhi,yboundlo,yboundhi,
|
|
$ zboundlo,zboundhi
|
|
|
|
if (x.lt.xboundlo) x = x + xprd
|
|
if (x.ge.xboundhi) x = x - xprd
|
|
if (y.lt.yboundlo) y = y + yprd
|
|
if (y.ge.yboundhi) y = y - yprd
|
|
|
|
return
|
|
end
|
|
|
|
|
|
c RNG - compute in double precision, return single
|
|
|
|
real*4 function random(iseed)
|
|
real*8 aa,mm,sseed
|
|
parameter (aa=16807.0D0,mm=2147483647.0D0)
|
|
|
|
sseed = iseed
|
|
sseed = mod(aa*sseed,mm)
|
|
random = sseed/mm
|
|
iseed = sseed
|
|
|
|
return
|
|
end
|